A number of platforms have been developed for chemical and biological sensing including optical techniques such as infra-red absorption, surface plasmon resonance (SPR) sensors, florescence-based sensors, and several methods employing optical resonators. These optical resonator sensor designs are attractive solutions as they tend to have a small form factor and can be designed with high sensitivities. Optical resonator sensor platforms can be categorized into two groups: multimode whispering gallery devices and single mode waveguide resonator devices.
Whispering gallery mode (WGM) devices tend to focus on changes in optical absorption and the effect on the resonator quality factor. These devices have been used as sensors when incorporating a microsphere selected to measure optical absorption at a predetermined wavelength. Additionally, when coated with a film suitable for interacting with and binding analytes of interest, the resonator will experience a change in the Q-factor as analyte is bound to the resonator. The Q-factor is altered through increased loss such that a change in the intensity of the optical transmission spectrum coupled through the resonator can be observed. Other WGM sensors rely on an interaction between the resonator surface and a molecular species of interest to change the effective refractive index of the set of optical modes supported by the WGM resonator. The resulting change in phase and/or resonant wavelength of these optical modes can be measured.
Whispering gallery mode resonators, such as microspheres typically have Q values of 109 and higher. Although high Q values are advantageous, WGM resonators tend to support a dense optical spectrum of modes which increases the difficulty in tracking the resonant wavelength of one specific mode. As a result, WGM sensor designs tend to rely on sensing changes in optical intensity related to changes in the cavity Q. Thus, WGM resonators are more susceptible to signal to noise issues relating to small variations in optical intensity due to environmental factors and coupling variations as well as source and detector related intensity noise.
An additional drawback related to the large number of optical modes is that WGM must generally rely on self-referencing. This method of referencing relies on comparing two measurements taken at different times, one measurement before the interaction occurs and a second measurement after the endpoint of the interaction. For example, sensor measurements are usually measured by referencing a change in intensity resulting from interaction of the WGM resonator with a specific analyte to a prior baseline intensity measurement taken just before exposure of the resonator to the analyte. These measurements can experience error due to environmental effects occurring after the first measurement or by secondary interactions such as non-specific binding.
Optical resonators based on single mode waveguides generally have lower Q values than WGM resonators. However, they offer the advantage of supporting only a single transverse spatial optical mode. For example, a micro-ring resonator fabricated from a rectangular cross-section waveguide can be designed to support only the lowest order transverse spatial mode, which generally consists of one transverse electric (TE) polarized mode as well as a second transverse magnetic (TM) polarized mode. The resulting transfer function consists of a single set of TE and TM temporal modes at resonant wavelengths given byλi=2πrn/i where r is the ring radius, n is the optical waveguide effective index, and i is an integer.
Thus, a single mode resonator design for a sensor permits transmission of an optical signal through a waveguide such that is passes by and interacts with a resonator. Some of the light couples from waveguide to resonator such that the waveguide's transmission spectrum contains a dip in intensity corresponding to the resonator resonance. The shift in the dip of the transmission spectrum corresponds to a change in resonance resulting from specific binding of a material to the resonator surface. The shift is measured and compared to the shift seen in a second reference ring. Alternatively the relative difference in the resonance shifts observed for TE and TM polarized optical signals that are coupled to an optical resonator may be measured. In general, current single mode resonator devices focus on monitoring the position of the dip in the transmission spectrum of light traveling the through a waveguide.
The single mode resonator configuration shown in FIG. 1a is known as an all-pass filter design or a through configuration. In this example, whenever the wavelength of the input signal matches one of the resonances of the ring resonator light couples from the waveguide to the resonator. Light propagating within the resonator experiences some optical loss before coupling back to the through waveguide producing a dip in the transmission spectrum as shown in FIG. 1b. 
In this design, the strength of the signal is related to the optical loss experienced by light traversing the ring resonator. An optical resonator with near zero loss will result in a very shallow dip in the transmission spectrum. This limits the sensitivity of the detection algorithm as intense noise fluctuation may hide the real signal. Compensating for this limitation requires intentionally increasing the loss in the ring. However, a higher loss results in a lower cavity Q and a broader resonance which in turn increases the difficulty in determining the precise resonant wavelength. Thus, one would prefer to have both a narrow resonance (high Q) as well as a high signal to noise ratio to best monitor the resonator resonance.
Current existing designs determine a net resonance shift, Δλ, at the endpoint by measuring the resonant wavelength of an active sensing ring after exposure to a material of interest and comparing the result to either the resonance of same ring before exposure or to that of a second reference ring. This method is ideal for determining the refractive index of a sample exposed to the ring resonator sensor and does well in sensing the absence or presence of a specific material of interest. However, this arrangement is not well suited for determining the precise level or concentration of material from the resonance shift after a fixed time. For example, the relative concentration of the material of interest must be known before exposure to the ring sensor to ensure the choice of an adequate endpoint time in order to both avoid overexposure and saturation effects as well as underexposure and non-observance of the shift in resonance.
There are a number of prior art references describing biological and chemical sensors based on optical resonators. These optical resonator detection schemes may be categorized as using multimode whispering gallery resonators (i.e., microspheres, microdisks, . . . ) or single mode waveguide resonators (i.e., ring resonators). Techniques using devices rely on endpoint detection schemes where the shift in resonant wavelength is measured at the end of a fixed interval of time. As such, prior art methods do not provide for real time analysis.